Contacts of the helix formed by residues 241 - 251 (chain D) in PDB entry 6NFJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D TRP* 3.7 9.2 + - + -
240D HIS* 1.3 84.3 - - + +
242D PRO* 1.3 69.7 - - - +
243D TYR* 3.2 15.1 + - - +
244D LEU* 3.3 28.5 + - - +
245D VAL* 3.4 9.9 + - - +
299D THR* 2.8 22.2 + - + +
301D GLY* 3.0 31.2 + - - +
373D SER* 4.6 7.2 + - - +
377D ASN* 4.9 2.0 - - - +
378D ASN* 2.6 28.9 + - - -
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Residues in contact with PRO 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D ILE* 3.7 19.5 - - + -
240D HIS 3.8 0.2 - - - -
241D ASN* 1.3 84.6 - - - +
243D TYR* 1.3 65.7 + - - +
244D LEU 3.3 0.4 - - - -
245D VAL* 3.2 21.3 + - + +
246D ALA* 3.2 9.7 + - - +
273D LEU* 3.9 16.5 - - + +
298D ILE* 4.0 12.8 - - + -
299D THR 3.3 13.7 - - - +
300D LEU* 3.7 17.9 - - + -
330D PHE* 3.6 37.8 - - + -
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Residues in contact with TYR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ASN* 3.2 12.0 - - - +
242D PRO* 1.3 81.2 - - + +
244D LEU* 1.3 79.5 + - + +
246D ALA* 4.0 0.9 - - - +
247D TRP* 2.8 64.9 + + + +
301D GLY 4.9 2.5 - - - +
325D SER 4.1 2.5 - - - -
326D VAL* 3.7 49.4 - - + +
329D TRP* 3.6 33.5 - + - -
330D PHE* 3.5 17.2 - - + -
378D ASN* 3.6 13.0 - - - +
384D THR* 2.7 30.8 + - + -
385D MET* 4.0 3.0 - - + -
386D ALA 5.1 0.3 + - - -
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Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D TRP* 3.6 28.9 - - + -
241D ASN* 3.3 28.8 + - - +
242D PRO 3.3 0.2 - - - -
243D TYR* 1.3 93.5 - - + +
245D VAL* 1.3 65.9 + - - +
248D HIS* 3.0 49.2 + - + +
249D GLY 3.5 1.0 + - - -
255D HIS* 3.7 17.0 + - + +
377D ASN* 3.6 40.4 - - + +
378D ASN* 3.9 6.1 - - - +
384D THR* 4.0 1.8 - - + -
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Residues in contact with VAL 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D TYR* 4.0 23.8 - - + +
196D TRP* 3.3 39.7 - - + +
209D TRP* 4.6 9.0 - - + +
239D ILE* 4.5 7.0 - - + -
241D ASN 3.4 11.7 - - - +
242D PRO* 3.2 13.8 + - + +
244D LEU* 1.3 78.5 - - - +
246D ALA* 1.3 59.6 + - - +
249D GLY* 3.4 17.0 + - - -
250D TYR* 4.2 8.5 - - + -
255D HIS* 5.4 2.7 - - - -
256D ALA 4.7 5.7 - - - +
269D VAL* 4.8 1.1 - - + -
273D LEU* 3.9 16.2 - - + -
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Residues in contact with ALA 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D PRO 3.2 10.8 + - - +
243D TYR 4.2 0.7 - - - +
245D VAL* 1.3 78.5 - - - +
247D TRP* 1.3 64.5 + - - +
250D TYR* 3.0 27.7 + - - +
266D VAL* 3.4 29.3 - - - +
269D VAL* 3.7 23.8 - - + -
270D GLY* 3.9 9.0 - - - +
273D LEU* 4.7 0.2 - - + -
329D TRP* 4.1 11.7 - - + -
330D PHE* 4.8 0.7 - - + -
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Residues in contact with TRP 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D TYR* 2.8 58.2 + + + +
246D ALA* 1.3 74.5 - - - +
248D HIS* 1.3 77.8 + + + +
251D GLY* 2.8 34.4 + - - -
252D THR* 3.2 16.6 + - + +
266D VAL* 4.5 16.1 - - + +
267D TYR* 4.3 16.8 - + - -
325D SER 6.0 0.7 - - - -
329D TRP* 4.4 12.3 - + + -
383D ASN 3.3 23.3 + - - -
384D THR 3.4 8.3 + - - -
385D MET 5.4 5.6 - - - -
386D ALA* 5.6 8.7 - - + -
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Residues in contact with HIS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D LEU* 3.0 38.9 + - + +
247D TRP* 1.3 92.6 - + - +
249D GLY* 1.3 55.3 + - - +
252D THR* 3.5 12.5 + - + -
253D GLY 3.6 1.8 + - - -
254D MET* 2.9 33.2 + - + +
255D HIS* 2.7 53.5 + + + +
377D ASN 4.8 1.5 + - - -
380D LYS 5.3 0.4 - - - -
381D PRO* 3.9 17.0 - - + -
383D ASN* 4.1 7.0 - - - -
384D THR* 2.9 41.8 + - + +
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Residues in contact with GLY 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D LEU 3.5 0.8 + - - -
245D VAL 3.4 19.5 + - - -
247D TRP 3.2 0.6 - - - -
248D HIS* 1.3 80.5 - - - +
250D TYR* 1.3 68.0 + - - +
251D GLY 3.8 0.4 - - - -
253D GLY 4.7 0.9 - - - -
255D HIS* 3.6 13.0 - - - -
256D ALA 3.7 10.8 - - - -
257D PRO* 4.0 1.4 - - - +
258D GLY 3.3 7.8 + - - -
259D GLU 3.1 23.5 + - - -
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Residues in contact with TYR 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D GLN* 3.2 26.0 + - - -
207D GLY 4.1 8.1 + - - -
209D TRP* 4.6 8.8 + + + -
210D LYS* 4.0 15.1 - - + +
245D VAL* 4.2 9.2 - - + -
246D ALA 3.0 15.5 + - - +
249D GLY* 1.3 78.7 - - - +
251D GLY* 1.3 57.3 + - - +
257D PRO* 3.6 26.6 - - + +
259D GLU* 2.8 50.8 - - + +
262D ASN* 3.2 23.5 + - + +
265D ALA* 3.8 15.5 - - + -
266D VAL* 3.4 17.7 - - + +
269D VAL* 3.6 32.9 - - + +
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Residues in contact with GLY 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D TRP* 2.8 18.4 + - - -
250D TYR* 1.3 79.0 - - - +
252D THR* 1.3 62.3 + - - +
253D GLY 3.5 0.2 - - - -
260D LYS* 3.6 6.4 - - - +
261D GLY* 3.3 21.8 + - - -
266D VAL* 3.5 13.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il